Optimer Pharmaceuticals Inc.’s Dificid is on track to lead as many as five new antibiotics onto the market over the next three years as a surge in drug-resistant germs stokes the need for new medicines.

The biotechnology industry is starting to fill a critical public-health niche being mostly shunned by larger drugmakers. Since 2006, only three of 111 drugs cleared in the U.S. were antibiotics. Optimer, a San Diego company with no marketed products, may win U.S. approval by May 30 to sell Dificid, a drug that fights stomach infections, the company has said.

“Pharma abandoned the antibiotic space because they didn’t think there was enough of a revenue opportunity,” said Alan Carr, a New York-based analyst with Needham & Co. “A smaller, more manageable product with revenue under $1 billion is fine for a biotech company.”

Dificid may generate $500 million a year in sales, Carr said in a telephone interview. Other companies in final testing of drugs that may gain U.S. marketing approval by 2014 are: Trius Therapeutics Inc., based in San Diego; The Medicines Co., of Parsippany, New Jersey; Boston-based Paratek Pharmaceuticals Inc.; Cubist Pharmaceuticals Inc., of Lexington, Massachusetts; and closely held Durata Therapeutics of Morristown, New Jersey.

The first antibiotic-resistant germs appeared in the 1940s. Since then, at least 13 strains of bacteria impervious to some antibiotics have emerged, with one called MRSA the most common, according to the U.S. Centers for Disease Control and Prevention, in Atlanta.

100,000 Killed Yearly

Germs resistant to one or more drugs kill 100,000 U.S. hospital patients a year and cost the health-care system more than $34 billion, according to the Infectious Disease Society of America, based in Arlington, Virginia.

“We desperately need drugs that can treat bugs that are resistant to everything, or almost everything, available,” said Brad Spellberg, an associate professor at the David Geffen School of Medicine at the University of California, Los Angeles, in a telephone interview.

Antibiotics have changed the world since 1928, when researchers learned by accident that penicillium mold had an antibacterial effect. By the 1940s, penicillin was treating soldiers wounded in World War II and saving the lives of people with pneumonia, syphilis and diphtheria. Bacterial meningitis no longer killed 90 percent of infected children.

From 1942 to the mid-1970s, drugmakers rolled out 10 new types of antibiotics, each with unique targets and modes of action, a report by the Federation of American Scientists found.

Two Drugmakers

Since then, most new antibiotics have been modifications of old ones and, today, only two of the top six drugmakers by market value are developing antibiotics, spokesmen said.

That’s because the drugs are used for only weeks at a time, compared with years for medicines that treat chronic diseases. U.S. sales of the top five antibiotics were a combined $6 billion in 2010, according to IMS Health Inc., a Norwalk, Connecticut-based research company. Pfizer Inc.’s cholesterol pill Lipitor, designed to cut the chances of a heart attack, generated $5.3 billion in U.S. sales on its own.

Additionally, doctors are advised to limit antibiotic treatment because of concerns that overuse can spur resistance, actions that have an unintended effect on sales, said Hank McKinnell, who retired as chief executive officer at New York-based Pfizer in 2006, and now serves on Optimer’s board.

“It takes the incentives away to do the research and get them approved to then not have them used,” McKinnell said in a telephone interview.

Open Field

This lack of interest has left the field open for biotech companies, such as Optimer.

The company’s Dificid, backed unanimously by an FDA advisory panel April 5, would be the first drug in 25 years approved to treat Clostridium difficile, a bacterium linked to intestinal infections often caught in hospitals.

In trials, Dificid was as effective as existing medications at controlling infections, giving doctors a new option when resistance strikes. It was better at preventing recurrences.

Other biotechnology companies conducting late-stage testing on new antibiotics are likely to submit applications for approval about 2013, said Juan Sanchez, an analyst with Ladenburg Thalmann & Co. in New York.

Trius is studying its antibiotic torezolid to treat skin infections, said Chief Executive Officer Jeffrey Stein. It will compete with Pfizer’s Zyvox, an 11-year-old drug with $1.2 billion in 2010 sales, and may generate $600 million a year by 2020, said Sanchez, who sees approval in 2014.

More Potent

In early trials, torezolid was shown to be more potent and faster-acting than Zyvox, Stein said. While both are so-called oxazolidinones, the Trius drug has a different chemical structure that leaves it unaffected by a mutation that can enable bacteria to resist Zyvox, Sanchez said.

A visit to the skin infections clinic at San Francisco General Hospital shows the need for new drugs.

On a recent morning, David Young, the clinic’s director, was involved in a case in which the patient had a red, swollen abscess on his cheek. The patient, whom Young couldn’t identify because of federal privacy laws, previously had infections on his chest, neck and face, Young said.

While the man’s infections respond to the clindamycin, an oral generic antibiotic, “the bacteria will grow back” after each treatment, Young said. It becomes infected with any break in the skin, from a spider bite to a shaving nick, he said.

“It is akin to pulling all the weeds out of a field,” he said. “When you stop weeding, the weeds will always return.”

20% Won’t Heal

Today, about 20 percent of patients won’t heal with clindamycin or Bactrim, another antibiotic, Young said. For them, the hospital faces a choice: a 10-day course of Pfizer’s Zyvox at a cost of about $1,000, or use of an intravenous drug, vancomycin, which requires a hospital stay.

Cubist expects to start final trials by year’s end for CXA-201, which targets pneumonia, abdominal and urinary tract infections caused by gram-negative bacteria, said Steve Gilman, executive vice president for research and development.

Durata Therapeutics, a two-year-old closely held company, is testing dalbavancin, one of two so-called lipoglycopeptides in late-stage trials. The drugs are modified versions of an older class of antibiotic that breaks down the cell walls and membranes of bacteria.

Durata hopes to gain approval to market the drug in early 2014, CEO Paul Edick said in an e-mail.

Medicines Co. Treatment

The other similar treatment is oritavancin from Medicines Co., which plans to complete its trials in 2012 and file for approval in 2013, said Michael Mitchell, a company spokesman, in a telephone interview. Analysts expect it to have sales of as much as $300 million for skin infections, Mitchell said.

Paratek Pharmaceuticals Inc.’s omadacycline, licensed to Basel, Switzerland-based Novartis AG, is in late-stage trials for skin infections. The drug is an injectable derivative of tetracycline to be followed by pill forms. Further studies are planned in community-acquired pneumonia and drug-resistant forms of staph and strep bacteria.